Using NEAT, will the child of two parent genomes always have the same structure as the more fit parent?
Yes, if you follow the original implementation the children will inherit the topology from the most fit parent.

Keep in mind that the goal is to obtain a good population, maintaining the genetic diversity high but at the same time selecting the best individuals from the population; so, in theory you are allowed to give the topology you prefer to the children.

Here there is an example of an alternative topology inheritance in which a child gets the genes that lead to an excess node while another child gets only the genes that create a new connection.